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Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses

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Abstract

Soil microbes play important roles in plant growth and in the biogeochemical cycling of earth’s elements. However, the structure and functions of the microbial community associated with the growth of second-generation energy crops, such as Miscanthus, remain unclear. Thus, in this study, the composition and function of the bacterial and fungal communities associated with Miscanthus cultivation were analyzed by MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. The results of community composition and diversity index analyses showed that Miscanthus cultivation significantly altered the bacterial and fungal community composition and reduced bacterial and fungal diversity. In addition, Miscanthus cultivation increased the soil organic matter (SOM) and total nitrogen (TN) contents. The correlation analysis between microbial community composition and environmental factors indicated that SOM and TN were the most important factors affecting bacterial and fungal communities. Miscanthus cultivation could enrich the abundances of Pseudomonas, Rhizobium, Luteibacter, Bradyrhizobium, Phenylobacterium and other common plant-promoting bacteria, while also increasing Cladophialophora, Hymenula, Magnaporthe, Mariannaea, etc., which predicted corresponded to the saprotrophic, plant pathogenic, and pathotrophic trophic modes. The PICRUSt predictive analysis indicated that Miscanthus cultivation altered the metabolic capabilities of bacterial communities, including the metabolism of carbon, nitrogen, and phosphorus cycle. In addition, FUNGUIld analysis indicated that Miscanthus cultivation altered the fungal trophic mode. The effects of Miscanthus on the communities and function of bacteria and fungi varied among Miscanthus species. Miscanthus specie Xiangdi NO 1 had the greatest impact on soil bacterial and fungal communities, whereas Miscanthus specie Wujiemang NO 1 had the greatest impact on soil bacteria and fungi functions. The results of this study provide a reference for the composition and function of microbial communities during the growth of Miscanthus.

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Acknowledgements

This research was supported by the National Natural Science Foundation of China (Grant No. 41601332), the Key Research Project of Colleges and Universities of Henan Province Education Department (Grant No. 16A210012, 17A180032) and the Central Public-interest Scientific Institution Basal Research Fund: Study on the mechanism of cadmium accumulation in soil by rice controlled by heavy metal immobilized microorganism and organic materials.

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  1. Yan Chen and Wei Tian contributed equally to this work.

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  1. Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, Henan Engineering Technology Research Center for Mushroom-based Foods, School of Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China

    Yan Chen, Yang Shao, Ying-Jun Li, Li-An Lin, Ying-Jun Zhang, Hui Han & Zhao-Jin Chen

  2. Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China

    Wei Tian

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  1. Yan Chen
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Chen, Y., Tian, W., Shao, Y. et al. Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. Arch Microbiol 202, 1157–1171 (2020). https://doi.org/10.1007/s00203-020-01830-1

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